Showing papers by "University of Geneva published in 2021"
TL;DR: New functionalities and major improvements of the BUSCO software are presented, as well as the renewal and expansion of the underlying datasets in sync with the OrthoDB v10 release.
Abstract: Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.
1,181 citations
Daniel J. Klionsky1, Amal Kamal Abdel-Aziz2, Sara Abdelfatah3, Mahmoud Abdellatif4 +2980 more•Institutions (777)
TL;DR: In this article, the authors present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes.
Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
1,129 citations
University College London1, International Institute for Applied Systems Analysis2, University of Reading3, United Nations University4, University of London5, University of Colorado Boulder6, Umeå University7, Tsinghua University8, World Health Organization9, Cardiff University10, University of Geneva11, University of New England (United States)12, University of Birmingham13, Yale University14, University of Washington15, Northeastern University16, Virginia Tech17, University of Oxford18, University of York19, International Livestock Research Institute20, Cayetano Heredia University21, Harvard University22, Boston University23, University of Sussex24, Nelson Marlborough Institute of Technology25, Emory University26, Columbia University27, Autonomous University of Barcelona28, Technische Universität München29, University of Melbourne30, Iran University of Medical Sciences31, University of Exeter32, Imperial College London33, University of Sheffield34, European Centre for Disease Prevention and Control35, Universiti Malaysia Terengganu36, University of Santiago de Compostela37
TL;DR: TRANSLATIONS For the Chinese, French, German, and Spanish translations of the abstract see Supplementary Materials section.
886 citations
National Institute for Health Research1, University of London2, University of Auckland3, Anglia Ruskin University4, University of Cambridge5, Queen's University Belfast6, Sun Yat-sen University7, The Fred Hollows Foundation8, Mbarara University of Science and Technology9, Ministry of Health and Family Welfare10, University of Geneva11, St Thomas' Hospital12, Leeds Teaching Hospitals NHS Trust13, Southwest University of Visual Arts14, Orbis International15, International Agency for the Prevention of Blindness16, University of Cape Town17, University Hospitals Birmingham NHS Foundation Trust18, University of Michigan19, Emory University20, Johns Hopkins University21, Massachusetts Eye and Ear Infirmary22, University of São Paulo23, University of Nairobi24, Seva Foundation25, Tilganga Institute of Ophthalmology26, Heidelberg University27, University of New South Wales28, The George Institute for Global Health29, L V Prasad Eye Institute30, College of Health Sciences, Bahrain31, Muhimbili University of Health and Allied Sciences32, International Institute of Minnesota33, University of the West Indies34, University of Melbourne35, Kenya Medical Training College36, Federal University of São Paulo37, Capital Medical University38, Singapore National Eye Center39, National University of Singapore40, Pan American Health Organization41, Brien Holden Vision Institute42, University of Calabar43
TL;DR: In this paper, the authors defined eye health as maximised vision, ocular health, and functional ability, thereby contributing to overall health and wellbeing, social inclusion, and quality of life.
435 citations
Evgeny Epifanovsky, Andrew T.B. Gilbert1, Andrew T.B. Gilbert2, Xintian Feng3 +235 more•Institutions (54)
TL;DR: The Q-Chem quantum chemistry program package as discussed by the authors provides a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, and methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques.
Abstract: This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
360 citations
University Medical Center Groningen1, European Bioinformatics Institute2, Netherlands Cancer Institute3, Georgia Institute of Technology4, Leipzig University5, Johns Hopkins University6, University of Cambridge7, NHS Blood and Transplant8, Garvan Institute of Medical Research9, University of Tartu10, Ontario Institute for Cancer Research11, University of Washington12, Public Health Research Institute13, University of Chicago14, Greifswald University Hospital15, Ludwig Maximilian University of Munich16, University of Bristol17, Erasmus University Rotterdam18, University of Westminster19, Luleå University of Technology20, Royal Devon and Exeter Hospital21, Swiss Institute of Bioinformatics22, University of Lausanne23, University of Geneva24, University of Dundee25, Agency for Science, Technology and Research26, University of Queensland27, Leiden University Medical Center28, Radboud University Nijmegen29, University of Liège30, University of Oxford31, Menzies Research Institute32, Icahn School of Medicine at Mount Sinai33, Ikerbasque34, VU University Amsterdam35, Stanford University36, Turku University Hospital37, University of Turku38, Maastricht University39, Karolinska Institutet40, Utrecht University41, University of Helsinki42, National Institutes of Health43, Technische Universität München44, Wellcome Trust Sanger Institute45, German Cancer Research Center46, Westlake University47, University of New South Wales48
TL;DR: In this article, the authors performed cis-and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium.
Abstract: Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium. We detected cis-eQTL for 88% of genes, and these were replicable in numerous tissues. Distal trans-eQTL (detected for 37% of 10,317 trait-associated variants tested) showed lower replication rates, partially due to low replication power and confounding by cell type composition. However, replication analyses in single-cell RNA-seq data prioritized intracellular trans-eQTL. Trans-eQTL exerted their effects via several mechanisms, primarily through regulation by transcription factors. Expression of 13% of the genes correlated with polygenic scores for 1,263 phenotypes, pinpointing potential drivers for those traits. In summary, this work represents a large eQTL resource, and its results serve as a starting point for in-depth interpretation of complex phenotypes.
344 citations
TL;DR: Aghanim et al. as mentioned in this paper used the same data set to derive a 95% upper bound of 0.020 using the principal component analysis (PCA) model and uniform priors on the PCA mode amplitudes.
Abstract: Author(s): Aghanim, N; Akrami, Y; Ashdown, M; Aumont, J; Baccigalupi, C; Ballardini, M; Banday, AJ; Barreiro, RB; Bartolo, N; Basak, S; Battye, R; Benabed, K; Bernard, JP; Bersanelli, M; Bielewicz, P; Bock, JJ; Bond, JR; Borrill, J; Bouchet, FR; Boulanger, F; Bucher, M; Burigana, C; Butler, RC; Calabrese, E; Cardoso, JF; Carron, J; Challinor, A; Chiang, HC; Chluba, J; Colombo, LPL; Combet, C; Contreras, D; Crill, BP; Cuttaia, F; De Bernardis, P; De Zotti, G; Delabrouille, J; Delouis, JM; DI Valentino, E; DIego, JM; Dore, O; Douspis, M; Ducout, A; Dupac, X; Dusini, S; Efstathiou, G; Elsner, F; Enslin, TA; Eriksen, HK; Fantaye, Y; Farhang, M; Fergusson, J; Fernandez-Cobos, R; Finelli, F; Forastieri, F; Frailis, M; Fraisse, AA; Franceschi, E; Frolov, A; Galeotta, S; Galli, S; Ganga, K; Genova-Santos, RT; Gerbino, M; Ghosh, T; Gonzalez-Nuevo, J; Gorski, KM; Gratton, S; Gruppuso, A; Gudmundsson, JE; Hamann, J; Handley, W; Hansen, FK; Herranz, D; Hildebrandt, SR; Hivon, E; Huang, Z; Jaffe, AH; Jones, WC; Karakci, A; Keihanen, E; Keskitalo, R; Kiiveri, K; Kim, J; Kisner, TS | Abstract: In the original version, the bounds given in Eqs. (87a) and (87b) on the contribution to the early-time optical depth, (15,30), contained a numerical error in deriving the 95th percentile from the Monte Carlo samples. The corrected 95% upper bounds are: τ(15,30) l 0:018 (lowE, flat τ(15, 30), FlexKnot), (1) τ(15, 30) l 0:023 (lowE, flat knot, FlexKnot): (2) These bounds are a factor of 3 larger than the originally reported results. Consequently, the new bounds do not significantly improve upon previous results from Planck data presented in Millea a Bouchet (2018) as was stated, but are instead comparable. Equations (1) and (2) give results that are now similar to those of Heinrich a Hu (2021), who used the same Planck 2018 data to derive a 95% upper bound of 0.020 using the principal component analysis (PCA) model and uniform priors on the PCA mode amplitudes.
344 citations
University of Paris1, University of Geneva2, University of California, San Francisco3, Lou Ruvo Brain Institute4, Autonomous University of Barcelona5, university of lille6, Karolinska University Hospital7, Sahlgrenska University Hospital8, University of California, San Diego9, Columbia University10, University of Melbourne11, Brown University12, University of Southern California13
TL;DR: In 2018, the International Working Group presented what they consider to be the current limitations of biomarkers in the diagnosis of Alzheimer's disease and, on the basis of this evidence, they proposed recommendations for how biomarkers should and should not be used for diagnosing Alzheimer's diseases in a clinical setting as mentioned in this paper.
Abstract: In 2018, the US National Institute on Aging and the Alzheimer's Association proposed a purely biological definition of Alzheimer's disease that relies on biomarkers. Although the intended use of this framework was for research purposes, it has engendered debate and challenges regarding its use in everyday clinical practice. For instance, cognitively unimpaired individuals can have biomarker evidence of both amyloid β and tau pathology but will often not develop clinical manifestations in their lifetime. Furthermore, a positive Alzheimer's disease pattern of biomarkers can be observed in other brain diseases in which Alzheimer's disease pathology is present as a comorbidity. In this Personal View, the International Working Group presents what we consider to be the current limitations of biomarkers in the diagnosis of Alzheimer's disease and, on the basis of this evidence, we propose recommendations for how biomarkers should and should not be used for diagnosing Alzheimer's disease in a clinical setting. We recommend that Alzheimer's disease diagnosis be restricted to people who have positive biomarkers together with specific Alzheimer's disease phenotypes, whereas biomarker-positive cognitively unimpaired individuals should be considered only at-risk for progression to Alzheimer's disease.
309 citations
TL;DR: In both studies, anxiety and depression during the pandemic was greater in younger members, women, those with pre-existing mental/physical health conditions and individuals in socioeconomic adversity, even when controlling for pre-pandemicxiety and depression.
Abstract: Background The COVID-19 pandemic and mitigation measures are likely to have a marked effect on mental health. It is important to use longitudinal data to improve inferences. Aims
To quantify the prevalence of depression, anxiety and mental well-being before and during the COVID-19 pandemic. Also, to identify groups at risk of depression and/or anxiety during the pandemic. Method
Data were from the Avon Longitudinal Study of Parents and Children (ALSPAC) index generation (n = 2850, mean age 28 years) and parent generation (n = 3720, mean age 59 years), and Generation Scotland (n = 4233, mean age 59 years). Depression was measured with the Short Mood and Feelings Questionnaire in ALSPAC and the Patient Health Questionnaire-9 in Generation Scotland. Anxiety and mental well-being were measured with the Generalised Anxiety Disorder Assessment-7 and the Short Warwick Edinburgh Mental Wellbeing Scale. Results
Depression during the pandemic was similar to pre-pandemic levels in the ALSPAC index generation, but those experiencing anxiety had almost doubled, at 24% (95% CI 23–26%) compared with a pre-pandemic level of 13% (95% CI 12–14%). In both studies, anxiety and depression during the pandemic was greater in younger members, women, those with pre-existing mental/physical health conditions and individuals in socioeconomic adversity, even when controlling for pre-pandemic anxiety and depression. Conclusions
These results provide evidence for increased anxiety in young people that is coincident with the pandemic. Specific groups are at elevated risk of depression and anxiety during the COVID-19 pandemic. This is important for planning current mental health provisions and for long-term impact beyond this pandemic.
308 citations
University of Pennsylvania1, University of Toronto2, Cochrane Collaboration3, McMaster University4, Mahidol University5, Johns Hopkins University6, Albert Einstein College of Medicine7, NewYork–Presbyterian Hospital8, Columbia University9, McGill University10, Leiden University Medical Center11, Yale University12, Pontifical Catholic University of Chile13, Kaiser Permanente14, University of Geneva15, Washington University in St. Louis16, Ottawa Hospital Research Institute17, American University of Beirut18, St. Joseph's Healthcare Hamilton19, University of Guadalajara20, King Hussein Cancer Center21, University of Chicago22, University of Freiburg23
TL;DR: The evidence-based guidelines of the American Society of Hematology (ASH) are intended to support patients, clinicians, and other health care professionals in decisions about the use of anticoagulation for thromboprophylaxis for patients with COVID-19-related critical illness and acute illness who do not have confirmed or suspected venous thromboembolism (VTE) as mentioned in this paper.
263 citations
TL;DR: A review of the current knowledge of emerging SARS-CoV-2 variants, particularly those deemed VOC/Is: B.1.351, B.7, and P.1, can be found in the MEDLINE and BioRxiv databases as discussed by the authors.
Intermountain Healthcare1, Medical College of Wisconsin2, University of Geneva3, University of Iowa4, Utrecht University5, Leiden University Medical Center6, Inova Fairfax Hospital7, University of California, Davis8, UCLA Medical Center9, Ottawa Hospital Research Institute10, Uniformed Services University of the Health Sciences11
TL;DR: The 2nd update to the 9th edition of these guidelines is presented in this article, where the authors provide recommendations on 17 PICO (Population, Intervention, Comparator, Outcome) questions, four of which have not been addressed previously.
TL;DR: Encouraging sufficient levels of physical activity and reducing sedentary time can play a vital role in helping people to cope with a major stressful event, such as the COVID-19 pandemic.
Abstract: To assess whether changes in physical activity and sedentary behaviour during the COVID-19 lockdown are associated with changes in mental and physical health. Observational longitudinal study. Participants living in France or Switzerland responded to online questionnaires measuring physical activity, physical and mental health, anxiety, and depressive symptoms. Paired sample t-tests were used to assess differences in physical activity and sedentary behaviour before and during lockdown. Multiple linear regressions were used to investigate associations between changes in physical activity and changes in mental and physical health during lockdown. 267 (wave1) and 110 participants (wave2; 2 weeks later) were recruited. Lockdown resulted in higher time spent in walking and moderate physical activity (~10min/day) and in sedentary behaviour (~75min/day), compared to pre COVID-19. Increased physical activity during leisure time from week 2 to week 4 of lockdown was associated with improved physical health (β=.24, p=.002). Additionally, an increase in sedentary behaviour during leisure time was associated with poorer physical health (β=-.35, p=.002), mental health (β=-.25, p=.003), and subjective vitality (β=-.30, p=.004). Ensuring sufficient levels of physical activity and reducing sedentary time can play a vital role in helping people to cope with a major stressful event, such as the COVID-19 pandemic.
TL;DR: The article describes the philosophy of this programming framework and lists the models already implemented, and benchmark simulations are provided which serve as a proof of quality of the implemented core functionalities.
Abstract: We present the scope, concepts, data structures and application programming models of the open-source Lattice Boltzmann library Palabos. Palabos is a C++ software platform developed since 2010 for Computational Fluid Dynamics simulations and Lattice Boltzmann modeling, which specifically targets applications with complex, coupled physics. The software proposes a very broad modeling framework, capable of addressing a large number of applications of interest in the Lattice Boltzmann community, yet exhibits solid computational performance. The article describes the philosophy of this programming framework and lists the models already implemented. Finally, benchmark simulations are provided which serve as a proof of quality of the implemented core functionalities.
TL;DR: It is shown that such a signal can be explained by second-order gravitational waves produced during the formation of primordial black holes from the collapse of sizeable scalar perturbations generated during inflation.
Abstract: A theoretical analysis lays out a plausibility scenario for interpreting data reported recently by the NANOGrav collaboration in terms of gravitational waves produced during the formation of primordial black holes.
TL;DR: The Swiss Bioinformatics Resource Portal (expasy) as mentioned in this paper provides a portfolio of reliable and state-of-the-art resources for the storage, analysis and interpretation of biological data.
Abstract: The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss) creates, maintains and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and resources for the storage, analysis and interpretation of biological data. Through Expasy (https://www.expasy.org), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. In 2020, Expasy was redesigned through a user-centric approach, known as User-Centred Design (UCD), whose aim is to create user interfaces that are easy-to-use, efficient and targeting the intended community. This approach, widely used in other fields such as marketing, e-commerce, and design of mobile applications, is still scarcely explored in bioinformatics. In total, around 50 people were actively involved, including internal stakeholders and end-users. In addition to an optimised interface that meets users' needs and expectations, the new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources.
University of Calgary1, ETH Zurich2, Cooperative Institute for Research in Environmental Sciences3, Swiss Federal Institute for Forest, Snow and Landscape Research4, University of Washington5, University of Zurich6, University of Potsdam7, United States Geological Survey8, University of Minnesota9, University of Graz10, University of Natural Resources and Life Sciences, Vienna11, University of Toulouse12, University of Utah13, Heidelberg University14, University of Geneva15, University of Leeds16, Simon Fraser University17, Newcastle University18, University of Dayton19, University of Oslo20, Planetary Science Institute21, University of Alberta22, University of Grenoble23, University of Sheffield24, Indian Institute of Technology Indore25, University of Dundee26, UNESCO27, Jawaharlal Nehru University28, Stockholm International Water Institute29, University of British Columbia30, University of Exeter31, Kathmandu32, Wadia Institute of Himalayan Geology33, University of Kashmir34, University of Delhi35, International Centre for Integrated Mountain Development36, Utrecht University37, University of Chile38, Northumbria University39
TL;DR: In this paper, an analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27x106 m3 of rock and glacier ice collapsed from the steep north face of Ronti Peak.
Abstract: On 7 Feb 2021, a catastrophic mass flow descended the Ronti Gad, Rishiganga, and Dhauliganga valleys in Chamoli, Uttarakhand, India, causing widespread devastation and severely damaging two hydropower projects. Over 200 people were killed or are missing. Our analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27x106 m3 of rock and glacier ice collapsed from the steep north face of Ronti Peak. The rock and ice avalanche rapidly transformed into an extraordinarily large and mobile debris flow that transported boulders >20 m in diameter, and scoured the valley walls up to 220 m above the valley floor. The intersection of the hazard cascade with downvalley infrastructure resulted in a disaster, which highlights key questions about adequate monitoring and sustainable development in the Himalaya as well as other remote, high-mountain environments.
TL;DR: In this article, the authors reported the detection of more than 530 photons at energies above 100 teraelectronvolts and up to 1.4 PeV from 12 sources in the Galaxy.
Abstract: The extension of the cosmic-ray spectrum beyond 1 petaelectronvolt (PeV; 1015 electronvolts) indicates the existence of the so-called PeVatrons—cosmic-ray factories that accelerate particles to PeV energies. We need to locate and identify such objects to find the origin of Galactic cosmic rays1. The principal signature of both electron and proton PeVatrons is ultrahigh-energy (exceeding 100 TeV) γ radiation. Evidence of the presence of a proton PeVatron has been found in the Galactic Centre, according to the detection of a hard-spectrum radiation extending to 0.04 PeV (ref. 2). Although γ-rays with energies slightly higher than 0.1 PeV have been reported from a few objects in the Galactic plane3–6, unbiased identification and in-depth exploration of PeVatrons requires detection of γ-rays with energies well above 0.1 PeV. Here we report the detection of more than 530 photons at energies above 100 teraelectronvolts and up to 1.4 PeV from 12 ultrahigh-energy γ-ray sources with a statistical significance greater than seven standard deviations. Despite having several potential counterparts in their proximity, including pulsar wind nebulae, supernova remnants and star-forming regions, the PeVatrons responsible for the ultrahigh-energy γ-rays have not yet been firmly localized and identified (except for the Crab Nebula), leaving open the origin of these extreme accelerators. Observations of γ-rays with energies up to 1.4 PeV find that 12 sources in the Galaxy are PeVatrons, one of which is the Crab Nebula.
University of Geneva1, Royal Institute of Technology2, The Graduate Center, CUNY3, College of Staten Island4, Stanford University5, University of Oxford6, Ludwig Maximilian University of Munich7, Technische Universität München8, University of Texas at Austin9, Institute of Science and Technology Austria10, University of Massachusetts Amherst11
TL;DR: In this paper, the authors re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram.
TL;DR: In this article, a systematic review and meta-analysis of serological surveys for antibodies to SARS-CoV-2 have been reported worldwide, and the authors aimed to synthesise, combine, and assess this large corpus of data.
TL;DR: In this paper, the authors assessed the seroconversion rates and anti-SARS-CoV-2 spike protein antibody titers following the first and second dose of BNT162b2 and mRNA-1273 vaccines in patients with cancer in US and Europe from January to April 2021.
TL;DR: In this article, the authors present an overview of a next-generation instrument, IceCube-Gen2, which will sharpen our understanding of the processes and environments that govern the Universe at the highest energies.
Abstract: The observation of electromagnetic radiation from radio to γ-ray wavelengths has provided a wealth of information about the Universe. However, at PeV (1015 eV) energies and above, most of the Universe is impenetrable to photons. New messengers, namely cosmic neutrinos, are needed to explore the most extreme environments of the Universe where black holes, neutron stars, and stellar explosions transform gravitational energy into non-thermal cosmic rays. These energetic particles havemillions of times higher energies than those produced in the most powerful particle accelerators on Earth. As neutrinos can escape from regions otherwise opaque to radiation, they allow an unique view deep into exploding stars and the vicinity of the event horizons of black holes. The discovery of cosmic neutrinos with IceCube has opened this new window on the Universe. IceCube has been successful in finding first evidence for cosmic particle acceleration in the jet of an active galactic nucleus. Yet, ultimately, its sensitivity is too limited to detect even the brightest neutrino sources with high significance, or to detect populations of less luminous sources. In thiswhite paper, we present an overview of a next-generation instrument, IceCube-Gen2, which will sharpen our understanding of the processes and environments that govern the Universe at the highest energies. IceCube-Gen2 is designed to: (a) Resolve the high-energy neutrino sky from TeV to EeV energies (b) Investigate cosmic particle acceleration through multi-messenger observations (c) Reveal the sources and propagation of the highest energy particles in the Universe (d) Probe fundamental physics with high-energy neutrinos IceCube-Gen2 will enhance the existing IceCube detector at the South Pole. It will increase the annual rate of observed cosmic neutrinos by a factor of ten compared to IceCube, and will be able to detect sources five times fainter than its predecessor. Furthermore, through the addition of a radio array, IceCube- Gen2 will extend the energy range by several orders of magnitude compared to IceCube. Construction will take 8 years and cost about $350M. The goal is to have IceCube-Gen2 fully operational by 2033. IceCube-Gen2 will play an essential role in shaping the new era of multimessenger astronomy, fundamentally advancing our knowledge of the highenergy Universe. This challenging mission can be fully addressed only through the combination of the information from the neutrino, electromagnetic, and gravitational wave emission of high-energy sources, in concert with the new survey instruments across the electromagnetic spectrum and gravitational wave detectors which will be available in the coming years.
TL;DR: The ESPRESSO spectrograph as discussed by the authors was designed for ultra-high radial-velocity (RV) precision and extreme spectral fidelity with the aim of performing exoplanet research and fundamental astrophysical experiments with unprecedented precision and accuracy.
Abstract: Context. ESPRESSO is the new high-resolution spectrograph of ESO’s Very Large Telescope (VLT). It was designed for ultra-high radial-velocity (RV) precision and extreme spectral fidelity with the aim of performing exoplanet research and fundamental astrophysical experiments with unprecedented precision and accuracy. It is able to observe with any of the four Unit Telescopes (UTs) of the VLT at a spectral resolving power of 140 000 or 190 000 over the 378.2 to 788.7 nm wavelength range; it can also observe with all four UTs together, turning the VLT into a 16 m diameter equivalent telescope in terms of collecting area while still providing a resolving power of 70 000.Aims. We provide a general description of the ESPRESSO instrument, report on its on-sky performance, and present our Guaranteed Time Observation (GTO) program along with its first results.Methods. ESPRESSO was installed on the Paranal Observatory in fall 2017. Commissioning (on-sky testing) was conducted between December 2017 and September 2018. The instrument saw its official start of operations on October 1, 2018, but improvements to the instrument and recommissioning runs were conducted until July 2019.Results. The measured overall optical throughput of ESPRESSO at 550 nm and a seeing of 0.65″ exceeds the 10% mark under nominal astroclimatic conditions. We demonstrate an RV precision of better than 25 cm s−1 during a single night and 50 cm s−1 over several months. These values being limited by photon noise and stellar jitter shows that the performance is compatible with an instrumental precision of 10 cm s−1 . No difference has been measured across the UTs, neither in throughput nor RV precision.Conclusions. The combination of the large collecting telescope area with the efficiency and the exquisite spectral fidelity of ESPRESSO opens a new parameter space in RV measurements, the study of planetary atmospheres, fundamental constants, stellar characterization, and many other fields.
TL;DR: Informing patients and physicians about COVID-19 symptom evolution and persistence in an outpatient setting in Geneva, Switzerland, from day 1 through day 30 to 45 after diagnosis may help them recognize the time course of the disease.
Abstract: Background: Coronavirus disease 2019 (COVID-19) has spread, causing a worldwide pandemic, and prolonged effects are emerging (1, 2). The term “long COVID” describes illness in persons who continue to report lasting effects after infection (3, 4). To date, little information exists about outpatient settings in this novel disease where 81% of cases are reportedly on the mild end of the spectrum (5). Informing patients and physicians about COVID-19 symptom evolution may help them recognize the time course of the disease, legitimize patients' concerns, and reassure them when possible. Messages around potentially persisting symptoms could also assist in reinforcing public health measures to avoid the spread of infection. Objective: To describe COVID-19 symptom evolution and persistence in an outpatient setting in Geneva, Switzerland, from day 1 through day 30 to 45 after diagnosis.
TL;DR: In this article, the authors compile current published reports on nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), evaluate the role of healthcare workers (HCWs) in transmission, and evaluate outbreak management practices.
Abstract: To compile current published reports on nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), evaluate the role of healthcare workers (HCWs) in transmission, and evaluate outbreak management practices.
Narrative literature review.
The coronavirus disease 2019 (COVID-19) pandemic has placed a large burden on hospitals and healthcare providers worldwide, which increases the risk of nosocomial transmission and outbreaks to “non-COVID” patients or residents, who represent the highest-risk population in terms of mortality, as well as HCWs. To date, there are several reports on nosocomial outbreaks of SARS-CoV-2, and although the attack rate is variable, it can be as high as 60%, with high mortality. There is currently little evidence on transmission dynamics, particularly using genomic sequencing, and the role of HCWs in initiating or amplifying nosocomial outbreaks is not elucidated. There has been a paradigm shift in management practices of viral respiratory outbreaks, that includes widespread testing of patients (or residents) and HCWs, including asymptomatic individuals. These expanded testing criteria appear to be crucial in identifying and controlling outbreaks.
TL;DR: The Alpha Magnetic Spectrometer (AMS) is a precision particle physics detector on the International Space Station (ISS) conducting a unique, long-duration mission of fundamental physics research in space as mentioned in this paper.
TL;DR: PHQ-9 has been widely validated and is recommended in a two-stage screening process, and longitudinal studies are necessary to provide evidence of long-term screening effectiveness.
TL;DR: The fourth edition of the International Code of Phytosociological Nomenclature (ICPN) was published by the Steering Committee of the IAVS Working Group for PhytoSociological nomenclatures (GPN) as mentioned in this paper.
Abstract: The fourth edition of the International Code of Phytosociological Nomenclature (ICPN) was prepared by the Steering Committee of the IAVS Working Group for Phytosociological Nomenclature (GPN). The edition consists of 14 Definitions, 7 Principles, 53 Articles, and 7 Appendices. When compared with the previous edition, the main amendments are: (a) the acceptance of electronic publications (Art. 1); (b) the introduction of binding decisions (Definition XIV, Principle II, Articles 1, 2b, 3c, 29b, 40, 42, 44, Appendices 6 and 7); (c) the mandatory use of the English or Latin terminology for syntaxonomic novelties (Definition II, Principle II, Articles 3d and 3i); (d) the introduction of autonyms for the main ranks when the corresponding secondary ranks are created (Articles 13b and 24); (e) the automatic correction of the taxon names (name‐giving taxa) used in the names of syntaxa in accordance with the International Code of Nomenclature for algae, fungi, and plants (ICN) (Article 44); (f) the possibility to mutate the name of a syntaxon in using other correct, alternative names for the name‐giving taxa (Article 45); (g) the introduction of inadequate names, a new category of rejected names (Definition V, Articles 43 through 45); and (h) the introduction of a conserved type (Definition XIII, Article 53). The fourth edition of ICPN was approved by the GPN on 25 May 2019 and becomes effectively binding on 1 January 2021.
TL;DR: In this paper, the authors highlight recent evidence of collective behaviors induced by higher-order interactions and outline three key challenges for the physics of higher order complex networks, which is the main paradigm for modeling the dynamics of interacting systems.
Abstract: Complex networks have become the main paradigm for modelling the dynamics of interacting systems. However, networks are intrinsically limited to describing pairwise interactions, whereas real-world systems are often characterized by higher-order interactions involving groups of three or more units. Higher-order structures, such as hypergraphs and simplicial complexes, are therefore a better tool to map the real organization of many social, biological and man-made systems. Here, we highlight recent evidence of collective behaviours induced by higher-order interactions, and we outline three key challenges for the physics of higher-order systems. Network representations of complex systems are limited to pairwise interactions, but real-world systems often involve higher-order interactions. This Perspective looks at the new physics emerging from attempts to characterize these interactions.
TL;DR: In this paper, a suite of five state-of-the-art binary black hole population models covering a range of isolated and dynamical formation channels was used to infer branching fractions between channels and constraints on uncertain physical processes that impact the observational properties of mergers.
Abstract: The second LIGO–Virgo catalog of gravitational-wave (GW) transients has more than quadrupled the observational sample of binary black holes. We analyze this catalog using a suite of five state-of-the-art binary black hole population models covering a range of isolated and dynamical formation channels and infer branching fractions between channels as well as constraints on uncertain physical processes that impact the observational properties of mergers. Given our set of formation models, we find significant differences between the branching fractions of the underlying and detectable populations, and the diversity of detections suggests that multiple formation channels are at play. A mixture of channels is strongly preferred over any single channel dominating the detected population: an individual channel does not contribute to more than sime70% of the observational sample of binary black holes. We calculate the preference between the natal spin assumptions and common-envelope efficiencies in our models, favoring natal spins of isolated black holes of lesssim0.1 and marginally preferring common-envelope efficiencies of gsim2.0 while strongly disfavoring highly inefficient common envelopes. We show that it is essential to consider multiple channels when interpreting GW catalogs, as inference on branching fractions and physical prescriptions becomes biased when contributing formation scenarios are not considered or incorrect physical prescriptions are assumed. Although our quantitative results can be affected by uncertain assumptions in model predictions, our methodology is capable of including models with updated theoretical considerations and additional formation channels.